Department of Biology, Indiana University, Bloomington, Indiana, USA.
School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana, USA.
mBio. 2019 Jul 2;10(4):e01226-19. doi: 10.1128/mBio.01226-19.
Mutation accumulation experiments followed by whole-genome sequencing have revealed that, for several bacterial species, the rate of base-pair substitutions (BPSs) is not constant across the chromosome but varies in a wave-like pattern that is symmetrical about the origin of replication. The experiments reported here demonstrated that, in , several interacting factors determine the wave. The origin is a major driver of BPS rates. When it is relocated, the BPS rates in a 1,000-kb region surrounding the new origin reproduce the pattern that surrounds the normal origin. However, the pattern across distant regions of the chromosome is unaltered and thus must be determined by other factors. Increasing the deoxynucleoside triphosphate (dNTP) concentration shifts the wave pattern away from the origin, supporting the hypothesis that fluctuations in dNTP pools coincident with replication firing contribute to the variations in the mutation rate. The nucleoid binding proteins (HU and Fis) and the terminus organizing protein (MatP) are also major factors. These proteins alter the three-dimensional structure of the DNA, and results suggest that mutation rates increase when highly structured DNA is replicated. Biases in error correction by proofreading and mismatch repair, both of which may be responsive to dNTP concentrations and DNA structure, also are major determinants of the wave pattern. These factors should apply to most bacterial and, possibly, eukaryotic genomes and suggest that different areas of the genome evolve at different rates. It has been found in several species of bacteria that the rate at which single base pairs are mutated is not constant across the genome but varies in a wave-like pattern that is symmetrical about the origin of replication. Using as our model system, we show that this pattern is the result of several interconnected factors. First, the timing and progression of replication are important in determining the wave pattern. Second, the three-dimensional structure of the DNA is also a factor, and the results suggest that mutation rates increase when highly structured DNA is replicated. Finally, biases in error correction, which may be responsive both to the progression of DNA synthesis and to DNA structure, are major determinants of the wave pattern. These factors should apply to most bacterial and, possibly, eukaryotic genomes and suggest that different areas of the genome evolve at different rates.
突变积累实验结合全基因组测序表明，对于几种细菌物种，碱基对替换（BPS）的速率并非在整个染色体上保持恒定，而是以一种波状模式变化，这种模式以复制起点为中心对称。本文报道的实验表明，在 中，有几个相互作用的因素决定了波的形态。复制起点是 BPS 速率的主要驱动因素。当它被重新定位时，新起点周围 1000kb 区域内的 BPS 速率会重现围绕正常起点的模式。然而，染色体上遥远区域的模式保持不变，因此必须由其他因素决定。增加脱氧核苷三磷酸（dNTP）浓度会使波模式远离起点，这支持了这样一种假设，即与复制启动同时波动的 dNTP 池的波动有助于突变率的变化。核基质结合蛋白（HU 和 Fis）和末端组织蛋白（MatP）也是主要因素。这些蛋白质改变了 DNA 的三维结构，结果表明，当高度结构化的 DNA 被复制时，突变率会增加。校对和错配修复的错误校正偏差也是主要决定因素，这两种偏差都可能对 dNTP 浓度和 DNA 结构有反应。这些因素可能适用于大多数细菌，也可能适用于真核生物基因组，并表明基因组的不同区域以不同的速率进化。在几种细菌物种中发现，单碱基对突变的速率在整个基因组中不是恒定的，而是以一种波状模式变化，这种模式以复制起点为中心对称。我们以 作为模型系统，表明这种模式是由几个相互关联的因素造成的。首先，复制的时间和进程对决定波的形态很重要。其次，DNA 的三维结构也是一个因素，结果表明，当高度结构化的 DNA 被复制时，突变率会增加。最后，错误校正中的偏差，可能既对 DNA 合成的进展，也对 DNA 结构有反应，是波的形态的主要决定因素。这些因素应该适用于大多数细菌，也可能适用于真核生物基因组，并表明基因组的不同区域以不同的速率进化。
